Preprints

Srivastava A, Karpievitch YV, Eichten SR, Borevitz JO, Lister R (2017) HOME: A histogram based machine learning approach for effective identification of differentially methylated regions. bioRxiv 10.1101/228221, pdf

Ford E, Grimmer MR, Stolzenburg S, Bogdanović O, de Mendoza A, Farnham PJ, Blancafort P, Lister R (2017) Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation. bioRxiv 10.1101/170506, pdf


Publications

Knaupp AS*, Buckberry S*, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A, Alaei S, Firas J, Holmes ML, Nair SS, Clark SJ, Nefzger CM, Lister R#, Polo JM# (2017) Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming. Cell Stem Cell 10.1016/j.stem.2017.11.007

Nefzger CM, Rossello FJ, Chen J, Liu X, Knaupp AS, Firas J, Paynter JM, Pflueger J, Buckberry S, Lim SM, Williams B, Alaei S, Faye-Chauhan K, Petretto E, Nilsson SK, Lister R, Ramialison M, Powell DR, Rackham OJL#, Polo JM# (2017) Cell Type of Origin Dictates the Route to Pluripotency. Cell Reports 10.1016/j.celrep.2017.11.029, pdf

Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanović O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJC (2017) Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. Genome Biology 10.1186/s13059-017-1335-7, pdf

Liu X*, Nefzger CM*, Rossello FJ, Chen J, Knaupp AS, Firas J, Ford E, Pflueger J, Paynter JM, Chy HS, O'Brien CM, Huang C, Mishra K, Hodgson-Garms M, Jansz N, Williams SM, Blewitt ME, Nilsson SK, Schittenhelm RB, Laslett AL, Lister R, Polo JM (2017) Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. Nature Methods 10.1038/nmeth.4436, paper

Narsai R#, Gouil Q, Secco D, Srivastava A, Karpievitch YV, Liew LC, Lister R, Lewsey MG#, Whelan J (2017) Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination. Genome Biology 10.1186/s13059-017-1302-3, pdf

Valensisi C, Andrus C, Buckberry S, Jayavelu ND, Lund RJ, Lister R, Hawkins RD (2017) Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Cell Reports 20(6):1448-1462, pdf

Crisp PA, Ganguly D, Smith AB, Murray KD, Estavillo GM, Searle IR, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ (2017) Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis. Plant Cell 10.1105/tpc.16.00828, pdf

Bogdanović O and Lister R (2017) DNA methylation and the preservation of cell identity. Current Opinion in Genetics and Development 10.1016/j.gde.2017.06.007

Secco D, Whelan J, Rouached H, Lister R (2017) Nutrient stress-induced chromatin changes in plants. Current Opinion in Plant Biology 39:1-7, pdf

Kretzmann JA, Ho D, Evans CW, Plani-Lam JHC, Garcia-Bloj B, Mohamed AE, O'Mara ML, Ford E, Tan DEK, Lister R, Blancafort P, Norret M, Iyer KS (2017) Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA. Chemical Science 8(4):2923-2930, pdf

Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J (2017) Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re‐oxygenation. The Plant Journal 10.1111/tpj.13418. pubmed

Stuart T, Eichten SR, Cahn J, Karpievitch YK, Borevitz JO, Lister R (2016) Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. eLife 10.7554/eLife.20777, pdf

Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO (2016) DNA methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity. Genome Research 10.1101/gr.205468.116. pdf, pubmed

Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanović O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538:336-43. pdf

Van Aken O, Ford E, Lister R, Huang S, Millar AH (2016) Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance. The Plant Journal 10.1111/tpj.13276. pubmed

Kawakatsu T*, Stuart T*, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R#, Benfey PN#, Ecker JR# (2016) Unique cell-type-specific patterns of DNA methylation in the root meristem. Nature Plants 10.1038/nplants.2016.58. journal

Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J (2016) Epigenomic Landscapes of Retinal Rods and Cones. eLife 10.7554/eLife.11613. journal

Bogdanović O#, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJC, Manzanares M, Sauka-Spengler T, Ecker JR, Vermeulen M#, Gómez-Skarmeta JL#, Lister R# (2016) Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nature Genetics 10.1038/ng.3522. journal

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanović O, Lister R, Veenstra GJ (2015) Embryonic transcription is controlled by maternally defined chromatin state. Nature Communications 10.1038/ncomms10148. pdf

Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M (2015) methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinformatics 10.1186/s12859-015-0742-6. pdf

Secco D#, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J#, Lister R# (2015) Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. eLife 10.7554/eLife.09343, pdf

Lister R and Mukamel EA (2015) Turning over DNA methylation in the mind. Frontiers in Neuroscience 10.3389/fnins.2015.00252. pdf

Mo A*, Mukamel EA*, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski Tj, Lister R, Eddy SR, Ecker JR, Nathans J (2015) Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron 86:1369–84. pdf

Roadmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317-30. pdf

Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR (2015) MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols 10:475-83. pdf

Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker JR, Muegge K (2014) Genome wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. Genome Research, gr.172015.114. pubmed

Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ (2014) Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Research, advanced online publication. pdf

Welch MD, Lister R (2014) Epigenomics and the control of fate, form and function in social insects. Current Opinion in Insect Science 1:31-8. COIS

Yu W, Briones V, Lister R, McIntosh C, Han Y, Lee EY, Ren J, Terashima M, Leighty RM, Ecker JR, Muegge K (2014) CG hypomethylation in Lsh−/− MEFs is associated with de novo H3K4me1 formation and altered cellular plasticity. PNAS 111(16):5890-5. pubmed

Looney T, Lee JH, Zhang L, Chen CH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker S, Fernandes C, Gaetz J, Foshay K, Clift K, Zhang Z, Li WQ, Vallender E, Wagner U, Qin JY, Michelini K, Bugarija B, Park D, Aryee E, Stricker T, White K, Ren B, Schroth G, Ecker J, Xiang AP, Zhou J, Lahn B. (2013) Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Research 24(2):267-80. pubmed

Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. (2013) STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics 29(24):3204-10. pubmed

Lister R*#, Mukamel EA*, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork A, Schultz MD, Tonti-Filippini J, Yu M, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM#, Ecker JR#. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341(6146):1237905. pubmed abstract perspective

Xie W, Schultz M*, Lister R*, Hou Z*, Rajagopal N*, Ray P*, Whitaker JW*, Tian S*, Hawkins RD*, Leung D*, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell 153(5):1134-48. pubmed abstract

Wierzbicki AT*, Cocklin R*, Mayampurath A*, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS. (2012) Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes and Development 26(16):2461825-36. pubmed pdf

Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. (2012) Widespread dynamic DNA methylation in response to biotic stress. PNAS 109(32):E2183-91. pubmed pdf

Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. (2011) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research 22(2):246-58. pubmed pdf

Pastor WA*, Pape UJ*, Huang Y*, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, Agarwal S, Rao A. (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473(7347):394-397. pubmed pmc

Lister R*, Pelizzola M*, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336):68-73. pubmed pdf

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology 28(10):1026-1028. pubmed pmc

Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 7;6(5):479-91. pubmed pdf

Lister R*, Pelizzola M*, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315-22. pubmed pmc

Sappl PG, Carroll AJ, Clifton R, Lister R, Whelan J, Harvey Millar A, Singh KB. (2009) The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress. Plant Journal 58(1):53-68. pubmed pdf

Lister R, Ecker JR. (2009) Finding the fifth base: Genome-wide sequencing of cytosine methylation. Genome Research 19(6):959-66. pubmed pdf

Lister R, Gregory BD, Ecker JR. (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Current Opinions in Plant Biology 12(2):107-18. pubmed pdf

Lister R*, O'Malley RC*, Tonti-Filippini J*, Gregory BD, Berry CC, Millar AH, Ecker JR. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523-36. pubmed pdf

Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Developmental Cell 14(6):854-66. pubmed pdf

Ho LH, Giraud E, Uggalla V, Lister R, Clifton R, Glen A, Thirkettle-Watts D, Van Aken O, Whelan J. (2008) Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis. Plant Physiology 147(4):1858-73. pubmed pdf

Lister R, Carrie C, Duncan O, Ho LH, Howell KA, Murcha MW, Whelan J. (2007) Functional definition of outer membrane proteins involved in preprotein import into mitochondria. Plant Cell 19(11):3739-59. pubmed pdf

Murcha MW, Elhafez D, Lister R, Tonti-Filippini J, Baumgartner M, Philippar K, Carrie C, Mokranjac D, Soll J, Whelan J. (2007) Characterization of the preprotein and amino Acid transporter gene family in Arabidopsis. Plant Physiology 143(1):199-212. pubmed pdf

Ho LHM, Giraud E, Lister R, Thirkettle-Watts D, Low J, Clifton R, Howell KA, Carrie C, Donald T, Whelan J. (2007) Characterisation of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide insensitive respiration during growth and development. Plant Physiology 143(1):199-212. pubmed pdf

Lister R, Whelan J. (2006) Mitochondrial protein import: convergent solutions for receptor structure. Current Biology 21;16(6):R197-9. pubmed pdf

Lister R, Hulett J, Lithgow T, Whelan J. (2005) Protein import into mitochondria: origins and functions today. Molecular Membrane Biology 22(1-2):87-100. pubmed

Clifton R, Lister R, Parker KL, Sappl PG, Elhafez D, Millar AH, Day DA, Whelan J. (2005) Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Molecular Biology 58:193-212. pubmed

Lister R, Chew O, Lee MN, Heazlewood JL, Clifton, R., Parker KL, Millar AH, Whelan J. (2004) A Transcriptomic and Proteomic Characterization of the Arabidopsis Mitochondrial Protein Import Apparatus and Its Response to Mitochondrial Dysfunction. Plant Physiology 134:777-789. pubmed pdf

Chew O, Lister R, Qbadou S, Heazlewood JL, Soll J, Schleiff E, Millar AH, Whelan, J. (2004) A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor. FEBS Letters 557:109-114. pubmed pdf

Murcha MW, Lister R, Ho AY, Whelan, J. (2003) Identification, expression, and import of components 17 and 23 of the inner mitochondrial membrane translocase from Arabidopsis. Plant Physiology 131:1737-1747. pubmed pdf

Lister R, Murcha MW, Whelan J (2003) The mitochondrial protein import machinery of plants (MPIMP) database. Nucleic Acids Research 31:325-327. pubmed pdf

Lister R, Mowday B, Whelan J, Millar AH (2002) Zinc dependent intermembrane space proteins stimulate carrier import into plant mitochondria. The Plant Journal 30:555-566. pubmed pdf

Lister R, Chew O, Rudhe C, Lee MN, Whelan J. (2001) Arabidopsis thaliana ferrochelatase-I and -II are not imported into Arabidopsis mitochondria. FEBS Letters 506: 291-295. pubmed pdf

*Equal contribution           #Co-corresponding author

2012